All Goddess Cube & Goddess Chest locations in Legend of Zelda: Skyward Sword HD
If you’re looking for extra items to aid you in your The Legend of Zelda: Skyward Sword HD quest, whether that be Rupees, Wallet upgrades, or Heart Pieces, you’re going to want to find all of the Goddess Cubes.
The Cubes are found on the Surface, and when struck with a Skyward Strike, will spawn a Goddess Chest in the Sky containing a reward. They’re scattered throughout the land and can be tricky to hunt down.

There are 27 Cubes and corresponding chests, with some needing certain upgrades and tools to reach so you won’t be able to claim all the loot until you’ve progressed in the game enough.
All Goddess Cube & Goddess Chest locations & rewards in Skyward Sword HD
You won’t be able to start collecting the Goddess Cubes until you’ve unlocked the Goddess Sword as you need to perform a Skyward Strike on them to spawn the chests. It’s pretty early on, though, so chances are, you’ve probably already got it.
The order of the 27 Cubes are as they should be collected in the story, taking upgrades and dungeon items into account:

Speak with Gorko the Goron
Outside of the Lumpy Pumpkin
Adventure Pouch upgrade
Just outside of Skyward Temple
On a small island by Pumpkin Landing
Heart Piece
Behind the Statue at Skyview Spring
Right on the top of the Lumpy Pumpkin
Gold Rupee
After entering, turn left and drop down to a ledge
Between Beedle’s Island and Bamboo Island

Silver Rupee
On the straight path after the Bird Statue
On a small island west of Fun Fun Island

Small Seed Satchel
(Restore the Light Tower first)
On a platform when gliding down the small volcano

On the right side of the Isle of Songs behind the building
(Need Digging Mitts)
Next to the Earth Temple, use a Bomb on the geyser to destroy the rocks
Directly behind the huge bamboo building on Bamboo Island
Directly to the east of the Earth Temple entrance down a ramp behind an enemy camp
On a small island southeast of Beedle’s Island. Climb across the vines
Treasure Medal
(Need the Water Dragon’s Scale)
On a ledge halfway down the giant sand slide
Jump in the Skyloft river and follow the passage
Head south from Bird Statue at the entrance of the mine
On an island southeast of Beedle’s Island. Use a bomb on the wall
(Need Hook Beetle)
In the south, bomb the Ampilus. Stand on its shell and run to the Cube
On the volcano-shaped island directly east of the Lanayru light beam
Heart Medal
In the north, hit the Timeshift Stone and ride the cart
Right at the top of the biggest cliff on Beedle’s Island
(Need Water Dragon’s Scale)
Swim inside of the Great Tree and look down once you exit
On a small island south of the Knight Academy in Skyloft
Swim into the Great Tree and walk around the back. Then glide to the Cube
On a small island east of the Lanayru light beam. Either skydive or use Clawshot
Swim into the Great Tree then exit. To the south, you’ll see a tightrope. Drop down and walk across
In the northeast section of the Thunderhead, kill the Walltulas on the vines and then climb up
Rupee Medal
(Need the Double Clawshots)
Make your way to the surfaced Bird Statue. Then turn around and walk straight ahead
Clawshot up the floating rocks in the west section of Skyloft. Dive off the northwest edge
(Need the Double Clawshots & Water Dragon’s Scale)
In the northeast section, blow up the wall and use the Clawshots on the targets
Jump in the water on the island west of Beedle’s Island. Do a water dash to land on the ledge
Use the Clawshots on the target southwest of the Lanayru Mining Facility
Go to the small island northwest of Fun Fun Island. Climb down the vines
Life Medal
Use the Clawshots on a box north of the entrance
Behind Gondo’s Scrap Shop in the Bazaar
Head just past the bridge with the Moblin then Clawshot onto the pillars
On an island northwest of Fun Fun Island. Clawshot through the gate
Potion Medal
At the entrance, Clawshot above the door and then to another target
In Skyloft, use the Clawshots on the floating rocks and grapple to the top
Above the entrance to Skyview Temple. Use your Clawshot on the target
On Beedle’s Island at night. Climb up the ladder to his bedroom
Outside of the Ancient Cistern, look up to see vines. Clawshot to them
Hiding on a tiny island directly beneath Fun Fun Island
By the waterfall, jump off the ledge and glide to the platform
On Bug Rock in the southwestern portion of the Thunderhead
Facing the Fire Sanctuary, hop out the left window and Clawshot
Right at the top of the main tower on the Isle of Songs in the Thunderhead
Small Bomb Bag
(Need the Mogma Mitts)
In the room directly to the right of the Volcano Summit entrance. Ride the platform
On the island southwest of the Isle of Songs. Use the Mogma Mitts on the dirt
In the northeast corner of Lanayru Gorge. Near where you plant the seedling